That works. And I found out, alternatively, I can turn of the fast water
definition by setting jfastw to 4.
What if I want to solvate a water cluster with a hydrophobic molecule in the
center into TIP3PBOX, say H2 + 4H2O or CO2+4H2O? I still need to load gaff,
right? But then the definition for the water molecules in the cluster might
screw things up. When I run simulation, it blows up within 10 steps, due to
extremely high bond energy and vdw energy. It is probably because the two
hydrogen atoms of each of the cluster water are too close to each other.
On Wed, Oct 13, 2010 at 8:01 AM, case <case.biomaps.rutgers.edu> wrote:
> On Tue, Oct 12, 2010, oscarjiao.gmail.com wrote:
> >
> > I've been playing with Antechamber and tleap lately. Got this error when
> I
> > was trying to solvate a single water molecule in a box of TIP3P waters.
> > Error: A residue defined as a "fast 3-point water" is not defined by a
> > triangle of three bonds. Residue 1 contains 2 bonds.
> >
> > The prmtop file shows the ATOM_TYPE of the alien water as oh ho ho, as
> > opposed to OW HW HW for the TIP3P water. What is the default model for a
> > water molecule in AMBER? Can I just force the water (solute) into a TIP3P
> > water.
>
> Don't use gaff for water, just solvate one WAT residue (TIP3P by default):
>
> >
> > source leaprc.ff99SB
> > solvateBox WAT TIP3PBOX 9
> > saveamberparm WAT prmtop inpcrd
>
> ...good luck....dac
>
>
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Received on Wed Oct 13 2010 - 10:00:07 PDT
